TarDB: A miRNA Target Database in Plants.


TarDB employs cross-species conservation filter, degradome and sRNA-seq data to identify high-confidence miRNA targets in plants.



miRNA ID

cru-miR161

Organism

Capsella rubella

Species

Mature miRNA Sequence(5'-3')

UUGAAAGUGACUACAUCGGGG

PmiREN

Precursor miRNA Sequence(5'-3')

TTATTGCGTCGATCAATGCATTGAAAGTGACTACATCGGGGCTCTGTGATTATACTTTTGCTCTCTCGCAAGGAGAAAAAAACAAATTAATCAGCCCCGGTTTAGTCACCTTCACTGCATTAATCAATGCATCTTGT

PmiREN

Precursor miRNA Structure(5'-3') 

--UUAU     C   C      U    A       C         CUGU     --UAC    GC     C 
      UGCGU GAU AAUGCA UGAA GUGACUA AUCGGGGCU    GAUUA     UUUU  UCUCU G
      ||||| ||| |||||| |||| ||||||| |||||||||    |||||     ||||  ||||| C
      ACGUA CUA UUACGU ACUU CACUGAU UGGCCCCGA    CUAAU     AAAA  AGAGG G
UGUUCU     A   A      C    C       U         ----     UAAAC    AA     A

Homologous Mature miRNAs   miRNAs are clustered by CD-HIT with sequence identity of >85% and word size of 5.

cru-miR161           UUGAAAGUGACUACAUCGGGG-
aly-miR161-5p.1      UUGAAAGUGACUACAUCGGGG-
ath-miR161.1         -UGAAAGUGACUACAUCGGGGU
aly-miR161-3p.1      -CCGGUUUAGUCACUUUCAC--
                            *    ** *